3/19	Solutions to Problem Set 4 have been posted: ppt pdf. We recommend the PowerPoint slides because they include explanatory notes.
3/13	The Friday 3/14 Problem Session is cancelled. Solutions to Problem set 4 will not be presented on Friday since not everyone will have turned in their solutions. Instead, we will release the solutions on the website once everyone's solutions are in.
3/12	Problem set 4 is due! Please either turn it in in class or email it to cs262.win08@gmail.com by 12:50 pm.
3/5	A scribing slot has opened up for March 10. If you would like to scribe this lecture, please email cs262.win08@gmail.com.
3/5	Problem set 3 has been graded! Come pick them up during officer hours, problem sessions, or lecture.
2/27	Problem set 4 has been posted.
2/27	Problem set 3 is due! Please either turn it in in class or email it to cs262.win08@gmail.com by 12:50 pm.
2/22	Problem set 2 has been graded! Come pick them up during officer hours, problem sessions, or lecture.
2/13	Problem set 3 has been posted.
2/13	Problem set 2 is due! Please either turn it in in class or email it to cs262.win08@gmail.com by 12:50 pm.
2/11	There was a mistake in the formulas in PS2 problem 1.c.iii. The formulas given in lecture are correct - please see the updated pdf.
2/6	Problem set 1 has been graded! Come pick them up during officer hours, problem sessions, or lecture.
2/2	Update: Slot filled! A scribing slot has opened up for March 3. If you would like to scribe this lecture, please email cs262.win08@gmail.com.
1/30	Problem set 1 is due! Please either turn it in in class or email it to cs262.win08@gmail.com by 12:50 pm.
1/30	Problem set 2 has been posted.
1/19	Scribing assignments have been made for all lectures.
1/16	Problem set 1 has been posted.
1/10	There will be no problem session on Friday January 11.
1/10	If you need help finding a group for collaborating on the problem sets, please email cs262.win08@gmail.com with a request.
1/10	If you would like to scribe one of the lectures, please email cs262.win08@gmail.com with the date you would like.

Genomics is a new and very active application area of computer science. The past ten years there has been an explosion of genomics data -- the entire DNA sequences of several organisms, including human, are now available. These are long strings of base pairs (A,C,G,T) containing all the information necessary for an organism's development and life. Computer science is playing a central role in genomics: from sequencing and assembling of DNA sequences to analyzing genomes in order to locate genes, repeat families, similarities between sequences of different organisms, and several other applications. The area of computational genomics includes both applications of older methods, and development of novel algorithms for the analysis of genomic sequences. This course aims to present some of the most basic and useful algorithms for sequence analysis, together with the minimal biological background necessary for a computer science student to appreciate their application to current genomics research. Sequence alignments, hidden Markov models, multiple alignment algorithms and heuristics such as Gibbs sampling, and the probabilistic interpretation of alignments will be covered. Applications of these tools to sequence analysis will be presented: comparing genomes of different species, gene finding, gene regulation, whole genome sequencing and assembly. Whenever possible, examples will be drawn from the most current developments in genomics research.

The following courses are recommended:

• CS161: Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts.

Durbin, Eddy, Krogh, Mitchison "Biological Sequence Analysis"

Gusfield "Algorithms on Strings, Trees, and Sequences"

1. Homework. Course will be graded based on the homeworks, NO FINAL. The course will have four challenging problem sets of equal size and grading weight. These must be handed in at the beginning of class on the due date, which will usually be two weeks after they are handed out. Recognizing that students may face unusual circumstances and require some flexibility in the course of the quarter, each student will have a total of three free late days (weekends are NOT counted) to use as s/he sees fit. Once these late days are exhausted, any homework turned in late will be penalized at the rate of 20% per late day (or fraction thereof). Under no circumstances will a homework be accepted more than three days after its due date.

   Late homeworks should be turned in to a member of the course staff, or, if none are available, placed under the door of S266 Clark Center. You must write the time and date of submission on the assignment. It is an honor code violation to write down the wrong time.Students with biological and computational backgrounds are encouraged to work together.

2. Scribing. Optionally, a student can scribe one lecture. Lecture notes will be due one week after the lecture date, and the grade on the lecture notes will substitute the two lowest-scoring problems in the homeworks. To ensure even coverage of the lectures, please sign up to scribe beforehand with one of the course staff.

Students may discuss and work on problems in groups of at most three people but must write up their own solutions. A student can be part of at most one group. If a student works individually, then the worst problem per problem set will be dropped. When writing up the solutions, students should write the names of people with whom they discussed the assignment. Also, when writing up the solutions students should not use written notes from group work.

Students are expected not to look at the solutions from previous years. Copying or intentionally refering to solutions from previous years will be considered an honor code violation.

Lecture: Monday Wednesday 12:50 - 2:05 pm in Skilling 193
Problem Sessions (optional): Friday 1:15 - 2:05 pm in McCullough 115

Serafim Batzoglou
Office: Clark Center S266
Office hours: Monday 2:15 - 3:30 pm in Clark Center S266
Phone: (650) 723-3334
Email: ude.drofnats@mifares (written backwards to avoid spam)

Andreas Sundquist
Office: Clark Center S260
Office hours: Thursdays noon - 2 pm in Clark Center S260
Phone: (650) 725-6094
Email: ude.drofnats@iuqdnusa

Marc Schaub
Office: Clark Center S260
Office hours: Tuesdays 1 - 3 pm in Gates B24A (phone during office hours: (650) 725-4385)
Phone: (650) 725-6094 (except during office hours)
Email: ude.drofnats@buahcs.cram

Questions should be sent to the course email address cs262.win08@gmail.com, or communicated to course staff in person after lecture or during office hours.

Some additional materials can be found Here

Below are the lecture notes from the Winter 2007 edition of this class. Please note that the content and order will not exactly correspond with this year's lectures. This year's lecture notes will be made available in the Schedule section below after they are submitted by the student scribing the lecture.

1	Introduction: Biology Background
2	Sequence Alignment--Dynamic Programming
3	Sequence Alignment Cont'd--Linear-Space Alignment;
4	Heuristic Local Aligners; Four-Russian Algorims
5	Hidden Markov Models--Decoding & Evaluation
6	Learning: EM / Baum-Welch
7	Learning cont'd
8	Pair HMMs for Sequence Alignment
9	DNA Sequencing
10	DNA Sequencing and Fragment Assembly
11	Cont'd Fragment Assembly
12	Molecular Evolution and Phylogenetic Trees
13	Multiple Sequence Alignment
14	Chaining of Local Alignments, Protein Profile HMMs and Classification
15	Gene Recognition
16	Gene Regulation, Microarrays
17	Motif Finding
18	Protein Interaction Networks
19	Protein Structure Prediction
20	RNA Secondary Structure Prediction

As the quarter progresses, the following schedule will be updated accordingly. Please check back often for the latest material.

	Date	Title	Reading	Homeworks	Scribe
1	1/9	Course overview, Basic biology, Sequence Alignment, Dynamic Programming			Clare Kasemset
2	1/14	Biology introduction	Durbin Chapters 1, 2 Gusfield Chapters 11, 12.1, 12.2, 12.7		Dipankar Bhatt Acharya
3	1/16	Sequence Alignment Cont'd--Linear-Space Alignment;		PS 1 out	Robin Zhou
4	1/21	No Class (Martin Luther King, Jr., Day)
5	1/23	Heuristic Local Aligners; Four-Russian Algorims			Chuang Peng
6	1/28	Hidden Markov Models--Decoding & Evaluation	Durbin Chapters 3, 4		Jason Auerbach
7	1/30	Learning: EM / Baum-Welch		PS 1 due PS 2 out	Huy Seng
8	2/4	Learning cont'd			Chung Ng
9	2/6	Pair HMMs for Sequence Alignment	Durbin Chapters 4		Hieu Nguyen
10	2/11	DNA Sequencing	ARACHNE, Euler, Genome sizes, transposons, genomic mapping--mathematical analysis		Patrick Shih
11	2/13	DNA Sequencing and Fragment Assembly		PS 2 due PS 3 out	Karan Mangla
12	2/18	No Class (Presidents' Day)
13	2/20	Cont'd Fragment Assembly	Gusfield Chapter 5 Genescan, Twinscan, EasyGene, SLAM		Fah Sathirapongsasuti
14	2/25	Molecular Evolution and Phylogenetic Trees			Saeed Hassanpour
15	2/27	Multiple Sequence Alignment	Gene Regulation and Motif Finding references below	PS 3 due PS 4 out	Sarim Baig
16	3/3	Chaining of Local Alignments, Protein Profile HMMs and Classification			Nuwan Seneratna
17	3/5	Gene Recognition	AVID, LAGAN		Khan Shing
18	3/10	Gene Regulation, Microarrays	Chaining: Gusfield 13.3, Multiple Alignment: suggested reading Gusfield 14.1, 14.2, 14.5, 14.5, 14.10.1-14.10.2 Durbin Chapter 6		Daniel Kluesing
19	3/12	Motif Finding		PS 4 due	Crystal Fong